Rice Genetics IV - IRRI books - International Rice Research Institute

ers, maps, mapping populations, and a P-1 derived artificial chromosome, PAC, library),the CCW has focused on sequencing the short arm of chromosome 10 (10s).Figure 4 shows the current physical map of the short arm of chromosome 10. We havemapped 31 contigs on 10s covering an estimated 75–85% of this arm. Twelve gapsremain, covering an estimated 2.6–4.0 Mb of DNA.An early surprise during the physical mapping of 10s was that the centromere wasmiss-mapped. In collaboration with J. Jiang (Cheng et al 2001), using fluorescence insitu hybridization, the chromosome 10 centromere was mapped between 15.2 cM and15.9 cM. This places it directly in the middle of the ~30 cM region assigned to CCW.Table 4 shows the current status of the CCW sequencing project. As shown, wehave submitted 6.1 Mb of assembled sequence to the HTGS section of Genbank andhave finished 1.39 Mb of rice DNA from nine BACs and submitted this to Genbank.All data are also available from the CUGI (www.genome.clemson.edu) and CSHL(http://nucleus.cshl.org/genseq) Web sites and the U.S. Rice Genome Sequencing andIRGSP Web site (http://www.usricegenome.org). As can be seen, CCW did not meetits year-one target of finishing and annotating 32 BACs because of several factors,such as the fact that the 30 cM assigned to CCW is highly heterochromatic and containsnumerous repeat regions that are difficult to finish. Further, most sequencinggroups have determined that rice is inherently difficult to finish and sequencing resultsin many GC (guanine cytosine) stops. To demonstrate the repeat nature of someof the BACs we have encountered, Figure 5 shows a Print Repeats/Miropeats (J.Parsons, http://www.ebi.ac.uk/~jparsons/) output of the repeat relationships of fourBACs on 10s. Rice BACs OSJNBa0035B06 and OSJNBa0053D03 are located nearthe centromeric region of 10s, whereas BACs OSJNBa0065H03 and OSJNBa0020E23are near 1.2 and 3.0 cM, respectively. Here we used a threshold of 500, which meansthat any repeat 500 bases or longer will be displayed. Figure 5 clearly shows that therepeat nature of the BACs near the centromere is much more complex than near thetelomere and will require a significant effort to finish.CCW has gained an intimate knowledge of and experience with the repeat natureof chromosome 10s and is confident that it will accomplish the finishing goals for theremainder of the project. In addition, at the Interim IRGSP Meeting held in Clemsonin September 2000, the IRGSP finishing problems were discussed and a new set offinishing guidelines was established to aid in resolving difficult regions of the ricegenome. These new guidelines will take effect in February 2001.Finishing the rice genomeThe original goal to finish the rice genome was 2008 (Sasaki and Burr 2000). In April2000, Monsanto announced that it had sequenced a 6X draft of about 3,000 BACsacross the rice genome and would share it with the IRGSP. The IRGSP is in the processof evaluating these new data; however, it is now apparent that just over half ofthe rice genome is covered by the Monsanto 6X draft. We are hopeful that, by combiningthe CUGI Rice Genome Framework with the Monsanto draft and the RiceGenome Program high-density genetic map, the IRGSP will be able to define a minimumtile of BAC clones across the entire rice genome. Such a tile would provideSequence-tagged connector/DNA fingerprint . . . 221